Research workbench
Crystal structure of medicago truncatula histidinol-phosphate phosphatase (mthpp) with intermolecular cross-link between LYS158 and CYS245
Analyse Crystal structure of medicago truncatula histidinol-phosphate phosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EQA
- Type
- protein
- Length
- 1,017 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase
- UniProt
- G7J7Q5
- Ligands
- CL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Inositol monophosphatase | protein | 254 | 36% helix, 26% strand | G7J7Q5 |
| B | Inositol monophosphatase | protein | 253 | 36% helix, 26% strand | G7J7Q5 |
| C | Inositol monophosphatase | protein | 256 | 35% helix, 26% strand | G7J7Q5 |
Ligands and binding sites
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.78 | 0.80 | 85 | empty |
| 2 | 474 | 0.71 | 0.81 | 39 | CL |
| 3 | 242 | 0.56 | 0.78 | 38 | empty |
| 4 | 208 | 0.55 | 0.79 | 33 | empty |
| 5 | 236 | 0.53 | 0.76 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1240 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 998 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 5EQA · Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt G7J7Q5
- Elsewhere: RCSB PDB 5EQA · PDBe 5EQA · UniProt G7J7Q5
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